Biosystems最新文献

{"title":"Reality and imagination intertwined: A sensorimotor paradox interpretation","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2024.105350","DOIUrl":"10.1016/j.biosystems.2024.105350","url":null,"abstract":"<div><div>As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105350"},"PeriodicalIF":2.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Universal dynamical function behind all genetic codes: P-adic attractor dynamical model","authors":"Ekaterina Yurova Axelsson,&nbsp;Andrei Khrennikov","doi":"10.1016/j.biosystems.2024.105353","DOIUrl":"10.1016/j.biosystems.2024.105353","url":null,"abstract":"<div><div>The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers <span><math><mrow><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>.</mo></mrow></math></span> This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function <span><math><mi>B</mi></math></span> such that the dynamical functions for all known genetic codes can be obtained from <span><math><mi>B</mi></math></span> by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by <span><math><mrow><mi>B</mi><mo>.</mo></mrow></math></span> We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from <span><math><mi>B</mi></math></span> through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105353"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Living cognition and the nature of organisms","authors":"Breno B. Just ,&nbsp;Sávio Torres de Farias","doi":"10.1016/j.biosystems.2024.105356","DOIUrl":"10.1016/j.biosystems.2024.105356","url":null,"abstract":"<div><div>There is no consensus about what cognition is. Different perspectives conceptualize it in different ways. In the same vein, there is no agreement about which systems are truly cognitive. This begs the question, what makes a process or a system cognitive? One of the most conspicuous features of cognition is that it is a set of processes. Cognition, in the end, is a collection of processes such as perception, memory, learning, decision-making, problem-solving, goal-directedness, attention, anticipation, communication, and maybe emotion. There is a debate about what they mean, and which systems possess these processes. One aspect of this problem concerns the level at which cognition and the single processes are conceptualized. To make this scenario clear, evolutionary and self-maintenance arguments are taken. Given the evolutive landscape, one sees processes shared by all organisms and their derivations in specific taxa. No matter which side of the complexity spectrum one favors, the similarities of the simple processes with the complex ones cannot be ignored, and the differences of some complex processes with their simple versions cannot be blurred. A final cognitive framework must make sense of both sides of the spectrum, their differences and similarities. Here, we discuss from an evolutionary perspective the basic elements shared by all living beings and whether these may be necessary and sufficient for understanding the cognitive process. Following these considerations, cognition can be expanded to every living being. Cognition is the set of informational and dynamic processes an organism must interact with and grasp aspects of its world. Understood at their most basic level, perception, memory, learning, problem-solving, decision-making, action, and other cognitive processes are basic features of biological functioning.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105356"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Techno-ethical concerns related to genetic sequencing reports","authors":"Zeki Topcu ,&nbsp;Sevil Zencir ,&nbsp;Matthis Krischel ,&nbsp;Heiner Fangerau","doi":"10.1016/j.biosystems.2024.105354","DOIUrl":"10.1016/j.biosystems.2024.105354","url":null,"abstract":"<div><div>Recombinant DNA technologies of the current era, most of which are comparable to past works of science fiction, have had diverse and significant impacts on social life. Among them, genetic sequencing deserves particular attention. The widespread use of genetic testing has raised numerous concerns regarding autonomy, confidentiality and privacy. In this context, the proliferation of ‘gene for X’ reports influences debates about the potentially beneficial or detrimental uses of genetics. While several studies have reported concerns related to the collection, storage and use of genetic data, few have considered the technical shortcomings that can affect the reliability of interpretation of sequencing data. In this essay, we will cover some of the current practices of genetic testing and safety aspects of DNA data. To evaluate the reliability of DNA data we will raise the question whether an ‘overestimation’ of researchers' results might reflect an ‘underestimation’ of our genetic make-up in terms of the limitations of the parameters necessary for the correct interpretation of genomic DNA. Following that question we will highlight the responsibility of researchers for proper science communication to avoid misleading information about genetic sequencing data.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105354"},"PeriodicalIF":2.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel amino acid distance matrices based on conductance measure","authors":"Nikola Štambuk ,&nbsp;Elena Fimmel ,&nbsp;Paško Konjevoda ,&nbsp;Krunoslav Brčić-Kostić ,&nbsp;Antonija Gračanin ,&nbsp;Hadi Saleh","doi":"10.1016/j.biosystems.2024.105355","DOIUrl":"10.1016/j.biosystems.2024.105355","url":null,"abstract":"<div><div>Ancestral relationships among biological species are often represented and analyzed by means of phylogenetic trees. Substitution and distance matrices are two main types of matrices that are used in phylogeny analyses. Substitution matrices describe a frequency change of amino acids in nucleotide or protein sequence over time, while distance matrices estimate phylogeny using a matrix of pairwise distances based on a particular code or analytical concept. Recent investigation by Elena Fimmel and coworkers (Life 11:1338, 2021) showed that: 1. the robustness of a genetic code against point mutations can be described using the conductance measure, and 2. all possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. In this article, we constructed and tested three novel distance matrices based on conductance measure, that take into account the point mutation robustness of the Standard Genetic Code (SGC). These distance matrices are based on maximum (CMAX), average (CAVG), and minimum (CMIN) conductance-optimized distances between codons coding for individual amino acids. The performance of those distance matrices was tested on a dataset of RecA proteins in <em>Bacteria</em>, <em>Archaea</em> (RadA homolog) and <em>Eukarya</em> (Rad51 homolog). RecA protein and its functional homologs were selected for this investigation since they are essential for the repair and maintenance of DNA, and consequently well conserved and present in all domains of life. PAM250 and BLOSUM62 matrices were usually used as a standard for distance matrix testing. PAM250 and BLOSUM62 substitution matrices specified accurately three biological domains of life according to Carl Woese and George Fox (Proc Natl Acad Sci U S A 74:5088, 1977). An identical result was obtained using three novel distance matrices (CMIN, CMAX, CAVG). This result supports the applicability of novel distance matrices based on the conductance method and suggests that further investigations based on this approach are justified.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105355"},"PeriodicalIF":2.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic code, the problem of coding biological cycles, and cyclic Gray codes","authors":"Sergey V. Petoukhov","doi":"10.1016/j.biosystems.2024.105349","DOIUrl":"10.1016/j.biosystems.2024.105349","url":null,"abstract":"<div><div>This article is devoted to the problem of genetically coding of inherited cyclic structures in biological bodies, whose life activity is based on a great inherited set of mutually coordinated cyclic processes. The author puts forward and arguments the idea that the genetic coding system is capable of encoding inherited cyclic processes because it itself is a system of cyclic codes connected with Boolean algebra of logic. In other words, the physiological processes in question are cyclical because they are genetically encoded by cyclic codes. In support of this idea, the author presents a set of his results on the connection of the genetic coding system with cyclic Gray codes, which are one of many known types of cyclic codes. This opens up the possibility of using for modeling inherited cyclic biostructures those algebraic and logical theories and constructions that are associated with Gray codes and have long been used in engineering technologies: Karnaugh maps, Hilbert curve, Hadamard matrices, Walsh functions, dyadic analysis, etc. The author believes that when studying the origin, evolution and function of the genetic code, it is necessary to take into account the ability of the genetic system to encode many mutually related cyclic processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105349"},"PeriodicalIF":2.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142433346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A mathematical framework for the statistical interpretation of biological growth models","authors":"A. Samoletov,&nbsp;B. Vasiev","doi":"10.1016/j.biosystems.2024.105342","DOIUrl":"10.1016/j.biosystems.2024.105342","url":null,"abstract":"<div><div>Biological entities are inherently dynamic. As such, various ecological disciplines use mathematical models to describe temporal evolution. Typically, growth curves are modelled as sigmoids, with the evolution modelled by ordinary differential equations. Among the various sigmoid models, the logistic, Gompertz and Richards equations are well-established and widely used for the purpose of fitting growth data in the fields of biology and ecology. The present paper puts forth a mathematical framework for the statistical analysis of population growth models. The analysis is based on a mathematical model of the population–environment relationship, the theoretical foundations of which are discussed in detail. By applying this theory, stochastic evolutionary equations are obtained, for which the logistic, Gompertz, Richards and Birch equations represent a limiting case. To substantiate the models of population growth dynamics, the results of numerical simulations are presented. It is demonstrated that a variety of population growth models can be addressed in a comparable manner. It is suggested that the discussed mathematical framework for statistical interpretation of the joint population–environment evolution represents a promising avenue for further research.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105342"},"PeriodicalIF":2.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From RNA to DNA: Emergence of reverse transcriptases from an ancestral RNA-dependent RNA polymerase","authors":"Sávio Torres de Farias ,&nbsp;Ana Karoline Nunes-Alves ,&nbsp;Marco José","doi":"10.1016/j.biosystems.2024.105345","DOIUrl":"10.1016/j.biosystems.2024.105345","url":null,"abstract":"<div><div>The transition from RNA as the informational molecule of primordial biological systems to the DNA genomes of modern organisms represents one of the greatest evolutionary transitions in the history of life. One way to understand this transition is to comprehend the origin of the enzymes responsible for the metabolism of nucleic acid polymers. In the present work, we reconstructed the ancestral sequence of RNA-dependent DNA polymerase (RdDp) and modeled its structure. The data demonstrate that, in terms of primary sequence, the ancestral sequences exhibit characteristic elements of RdDp; however, structurally, they are more similar to RNA-dependent RNA polymerase (RdRp). The presented data suggest that RdDp may have originated through modifications and neofunctionalization from an RdRp-like ancestor.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105345"},"PeriodicalIF":2.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reflexive neural circuits and the origin of language and music codes","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2024.105346","DOIUrl":"10.1016/j.biosystems.2024.105346","url":null,"abstract":"<div><div>Conscious activity is grounded in the reflexive self-awareness in sense perception, through which the codes signifying sensual perceptive events operate and constrain human behavior. These codes grow via the creative generation of hypertextual statements. We apply the model of Vladimir Lefebvre (Lefebvre, V.A., 1987, J. Soc. Biol. Struct. 10, 129–175) to reveal the underlying structures on which the perception and creative development of language and music codes are based. According to this model, the reflexive structure of conscious subject is grounded in three thermodynamic cycles united by the control of the basic functional cycle by the second one, and resulting in the internal action that it turn is perceived by the third cycle evaluating this action. In this arrangement, the generative language structures are formed and the frequencies of sounds that form musical phrases and patterns are selected. We discuss the participation of certain neural brain structures and the establishment of reflexive neural circuits in the <em>ad hoc</em> transformation of perceptive signals, and show the similarities between the processes of perception and of biological self-maintenance and morphogenesis. We trace the peculiarities of the temporal encoding of emotions in music and musical creativity, as well as the principles of sharing musical information between the performing and the perceiving individuals.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105346"},"PeriodicalIF":2.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"William Bateson, black slavery, eugenics and speciation: The relative roles of politics and science","authors":"Donald R. Forsdyke","doi":"10.1016/j.biosystems.2024.105348","DOIUrl":"10.1016/j.biosystems.2024.105348","url":null,"abstract":"<div><div>The peace of the world is challenged by societal confrontations that can often be labeled “racial” or “ethnic.” Emblematic of this is discrimination based on skin colour. William Bateson's background suggests sympathy with the black emancipation movement. Yet the movement's success is attributed more to battles between political figures than between scientists with contending views on the biology of racial differences. However, in the long term, Bateson's contributions to slavery and eugenic issues may be seen as no less important than those of politicians. Mendel's discovery of what we now know as “genes” languished until seized upon by Bateson in 1900. For six exhausting years he struggled to win scientific acceptance of these biological character-determining units. Later, he pressed the Mendelian message home to the general public, opposing simplistic applications of Mendelian principles to human affairs, and arguing that minor genic differences that distinguished “races” – e.g. skin colour – do not initiate new species. Bateson praised the “physiological selection” speciation hypothesis of Darwin's young research associate, George Romanes. This enthusiasm was rekindled by Robert Lock and formulated in modern terms with C. R. Crowther. Thus, the spark that initiates a divergence into two species can be non-genic. This normal form of hybrid sterility, based on genome-wide DNA sequence differences, operates on, but has not succeeded in dividing, the human species. It should not be labeled “idiopathic,” and be clearly distinguished both from pathological sterility and undiagnosed sterilities that may prove to be pathological. We are one reproductively isolated population, the human species.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105348"},"PeriodicalIF":2.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}